Windows doesn't work at the moment (on Ecoli K12)

[rmcolq]

Coming unstuck with a samtools line.

Originally code read:
samtools sort -o test/Ecoli_K12/reads_sorted.bam test/Ecoli_K12/reads.bam
[E::hts_open] fail to open file 'test/Ecoli_K12/reads_sorted.bam'
[bam_sort_core] fail to open file test/Ecoli_K12/reads_sorted.bam

Changed order to:
samtools sort test/Ecoli_K12/reads.bam -o test/Ecoli_K12/reads_sorted.bam
And got:
Segmentation fault (core dumped)
[test/Ecoli_K12=$base_dir]

It's been forever since I ran this bit of the code last. For another day now...